5HIX

Cocrystal structure of an anti-parallel DNA G-quadruplex and a tetra-Quinoline Foldamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report



Literature

Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.

Mandal, P.K.Baptiste, B.Langlois d'Estaintot, B.Kauffmann, B.Huc, I.

(2016) Chembiochem 17: 1911-1914

  • DOI: 10.1002/cbic.201600281
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antipar ...

    Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antiparallel hairpin dimeric DNA G-quadruplex (G 4 T 4 G 4 ) 2 with tetramer 1-a helically folded oligo-quinolinecarboxamide bearing cationic side chains-that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G 4 T 4 G 4 ) 2 in the solid state are observed.


    Organizational Affiliation

    Bordeaux Institut National Polytechnique, CBMN, UMR 5248), 2 rue Escarpit, 33600, Pessac, France. i.huc@iecb.u-bordeaux.fr.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
Dimeric G-quadruplexA, B12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
61Q
Query on 61Q

Download CCD File 
A
4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-nitroquinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinoline-2-carboxylic acid
C52 H52 N12 O11
PDPDTUNURBJNEI-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.701α = 90
b = 31.701β = 90
c = 97.373γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFranceERC-2012-AdG-320892

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release